6XUJ | pdb_00006xuj

HumRadA1 in complex with 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine in P21212

PDB DOI: https://doi.org/10.2210/pdb6XUJ/pdb

Classification: RECOMBINATION
Organism(s): Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-01-20 Released: 2021-03-03
Deposition Author(s): Marsh, M.E., Scott, D.E., Hyvonen, M.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.205 (Depositor), 0.208 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Optimising crystallographic systems for structure-guided drug discovery

Brear, P.B., Marsh, M., Hyvonen, M.

To be published.

Macromolecule Content

Total Structure Weight: 25.86 kDa
Atom Count: 2,089
Modeled Residue Count: 224
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair and recombination protein RadA	A	231	Pyrococcus furiosus DSM 3638	Mutation(s): 5 Gene Names: radA, PF1926
UniProt
Find proteins for O74036 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore O74036 Go to UniProtKB: O74036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O74036
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O1E (Subject of Investigation/LOI) Query on O1E Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine C₁₃ H₁₄ N₄ S UEBXWPXCTRZFCZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.205 (Depositor), 0.208 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.453	α = 90
b = 73.211	β = 90
c = 40.793	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	080083/Z/06/Z

Revision History (Full details and data files)

Version 1.0: 2021-03-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.